Clean out old files, especially from bin directories.

These will typically have a .bak or .old file extension. They usually represent binaries that we might want to keep around for awhile after installing a new version of a program, to make it possible to revert to the old version if necessary.

Review and document recent changes

All changes should be documented in BIRCHDEV/doc/ReleaseNotes.html

Update splash screen for BIRCH launcher

The file birch_white_version.png is displayed in the birch launcher, with the version number for the current version. This number needs to be updated in the graphic. See the instructions
in /home/psgendb/BIRCHDEV/dat/birch/hints_for_birch_white_version.txt.

Generate a new Development Release, including binaries

a. Revise graphics for birch launcher to show Development release number.

Once a new stable version of birch has been frozen,
Go to BIRCHDEV/dat/birch and follow the instructions in hints_for_birch_white_version.txt. For example, if the stable version is 3.30, version should be changed to 3.40D, to indicate the new Development version.

b. Edit BIRCHDEV/build/makeframework.excludefile to exclude all unnecessary files from the $birch/java directory. Mostly these are in the various bioLegato versions. Next, create a development version of the framework file:

makeframework.csh

Test Development Release on all supported platforms

solaris-sparc (antares)

solaris-amd64 (mira)

linux-x86_64 (mars, venus, jupiter)

linux-intel (Ubuntu i386vm on flamingo)

osx-x86_64 (albacore, peacock)

Generate a Stable Release, but don't list it on the download page.

a. Revise graphics for birch launcher to show stable release number.

Go to BIRCHDEV/dat/birch and follow the instructions in hints_for_birch_white_version.txt. For example, if the Development version is 3.30D, change that to 3.30, to indicate a stable version.

Binaries for linux-intel and osx-x86_64 must be generated on the brassica x86 VM and albacore, respectively, and uploaded to the Development directory.

c. Create a new birch framework

makeframework.csh -v version_number

This script creates a new snapshot called framework_version_number.tar gz. It also copies the tar archives containing the development version of the binaries to new files with the version number. This means that the binary files need to be up to date in the development verison before running makeframework.csh.

d. Add the new version number to birchtally.cgi

Login as birch on flamingo.

cd /usr/lib/cgi-bin/birch

Add the new version number to the list of valid versions in birchtally.cgi.

Versions = ['D', '3.00','2.96']

birchtally.cgi will fail to record a birch download if its version number is not in the list.

Test on other systems

as in step 3

When satisfied, change the symbolic link CURRENT to point to the new version.

eg.

cd /home/psgendb/FTP/BIRCH
ln -s 2.9 CURRENT

In this example, GetBirch will see version 2.9 as the current version for download.

v) If the mail message looks good, send it to the actual mailing list:

python mailer.py mailinglist.txt BIRCH3.10announcement.html

Mailing lists:

mailinglist.txt

mac.mailinglist.txt

MGCB2PIs.mailinglist

Note: It probably makes sense to send out announcements to the mailing lists one list per day. Usually in the first 24 hr. after a mailing, you get a few of Mail Delivery System messages saying that a user is not found. This way, you know which mailinglist to delete an email address from.

Before doing further announcements, give people a week or two to see if there are problems.

Other places to announce

BIRCH FaceBook page

Authors of programs incorporated in BIRCH - This could be a really big way to get people to use the package. This is especially true of programs that do not have GUIs. This should perhaps be a separate mailing list.

Facebook Bioinformatics page

bioinformatics.org

bioinformatics.ca

Linked-In

www.biostars.org

seqanswers.org

Teaching bioinformatics! - Let's find places that focus on teaching bioinformatics. A great deal of the potential for BIRCH is in teaching. This will be especially true at institutions that don't have huge budgets, but can afford a small server with free software. This could be the most effective way to increase the BIRCH user base.

How about an article in a teaching journal (or, a research journal that will publish teaching articles) eg. "Experiential bioinformatics - Using BIRCH to train 21st century biologists."